[English] 日本語
Yorodumi- PDB-4h76: Crystal structure of the catalytic domain of Human MMP12 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h76 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the catalytic domain of Human MMP12 in complex with a broad spectrum hydroxamate inhibitor | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | hydrolase/hydrolase inhibitor / Broad spectrum MMP hydroxamate inhibitor / METZINCIN / Zinc protease / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of interferon-alpha production / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to virus / metalloendopeptidase activity / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Stura, E.A. / Vera, L. / Cassar-Lajeunesse, E. / Nuti, E. / Dive, V. / Rossello, A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2013 Title: Crystallization of bi-functional ligand protein complexes. Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A. #1: Journal: J.Struct.Biol. / Year: 2013 Title: Crystallization of bi-functional ligand protein complexes. Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A. #2: Journal: Bioorg.Med.Chem. / Year: 2004 Title: New N-arylsulfonyl-N-alkoxyaminoacetohydroxamic acids as selective inhibitors of gelatinase A (MMP-2). Authors: Rossello, A. / Nuti, E. / Orlandini, E. / Carelli, P. / Rapposelli, S. / Macchia, M. / Minutolo, F. / Carbonaro, L. / Albini, A. / Benelli, R. / Cercignani, G. / Murphy, G. / Balsamo, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4h76.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4h76.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 4h76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h76_validation.pdf.gz | 849.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4h76_full_validation.pdf.gz | 851.1 KB | Display | |
Data in XML | 4h76_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4h76_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/4h76 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/4h76 | HTTPS FTP |
-Related structure data
Related structure data | 4h1qC 4h2eC 4h30C 4h3xC 4h49C 4h82C 4h84C 4hmaC 4i03C 3ljgS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17615.670 Da / Num. of mol.: 1 Fragment: Human MMP12 catalytic domain: unp residues 106-263 Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HME, MMP12 / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P39900, macrophage elastase |
---|
-Non-polymers , 7 types, 214 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-10B / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein:(hMMP12 F171D at 927 micro-M + acetohydroxamic acid at 11.6 milli-M Reservoir: 45% PEG 4,000 0.2 M imidazole piperidine Cryoprotection: 10% Di-ethylene glycol, 10% 1.2-propanediol, ...Details: Protein:(hMMP12 F171D at 927 micro-M + acetohydroxamic acid at 11.6 milli-M Reservoir: 45% PEG 4,000 0.2 M imidazole piperidine Cryoprotection: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10,000, 10% (AAB buffer 10% acid/90% basic) 0.2 M NaCl. Flash cooling in LN2. , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2011 / Details: bent cylindrical mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. all: 27511 / Num. obs: 27420 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.98 % / Biso Wilson estimate: 21.127 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.107 / Net I/σ(I): 14.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LJG Resolution: 1.5→46.758 Å / SU ML: 0.11 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Phase error: 17.1 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→46.758 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
|